2BWX

His354Ala Escherichia coli Aminopeptidase P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WL9PDB ENTRY 1WL9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5277HANGING DROP VAPOUR DIFFUSION AT 4C. 2 UL 10 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 32 % PEG 4K, 0.1 M TRIS PH 8.5. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10% MPD AND 1 MM MNCL2 FOR 30 MIN AT 4C PRIOR TO CRYOCOOLING.
Crystal Properties
Matthews coefficientSolvent content
4.471.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.252α = 90
b = 177.252β = 90
c = 96.77γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRRORS2005-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200H

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.776.71000.0716.55.997989621.17
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.791000.671.95.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1WL91.7154.39499029651000.1590.1580.176RANDOM18.59
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.120.060.12-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.339
r_dihedral_angle_4_deg14.078
r_dihedral_angle_3_deg10.781
r_dihedral_angle_1_deg5.997
r_scangle_it5.662
r_scbond_it3.855
r_mcangle_it2.29
r_mcbond_it2.065
r_angle_refined_deg1.183
r_angle_other_deg0.792
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.339
r_dihedral_angle_4_deg14.078
r_dihedral_angle_3_deg10.781
r_dihedral_angle_1_deg5.997
r_scangle_it5.662
r_scbond_it3.855
r_mcangle_it2.29
r_mcbond_it2.065
r_angle_refined_deg1.183
r_angle_other_deg0.792
r_symmetry_vdw_other0.3
r_symmetry_vdw_refined0.211
r_nbd_refined0.206
r_nbd_other0.177
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.125
r_nbtor_other0.079
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3501
Nucleic Acid Atoms
Solvent Atoms636
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling